Featured Research

from universities, journals, and other organizations

Biochemists Gain Crystal-Clear Insight Into 'Ancient' Enzyme

Date:

May 15, 1998

Source:

Duke University

Summary:

Biochemists from the University of Pennsylvania and Duke University Medical Center have reported analytical studies revealing unexpected new insights into how two very different molecules - a protein and an RNA - work together to form an enzyme that performs one of the fundamental tasks of constructing the protein-making machinery of the cell.

Share This

DURHAM, N.C. -- Biochemists from the University of Pennsylvania and Duke University Medical Center have reported analytical studies revealing unexpected new insights into how two very different molecules - a protein and an RNA - work together to form an enzyme that performs one of the fundamental tasks of constructing the protein-making machinery of the cell.

Related Articles

Their findings suggest that the partnership between the two molecules might represent an ancient remnant of an early era in life's evolution when RNA molecules were the enzymatic workhorses of primordial cells, before more versatile proteins evolved to take over the job.

The findings also may offer new targets for antibiotic compounds that could disrupt this key process in bacteria to kill them, the researchers said.

The biochemists reported in the May 1 issue of Science that they had obtained the crystal structure of the protein that is part of the enzyme "ribonuclease P." This enzyme is also known as a "ribozyme," because it is one in which the ribonucleic acid (RNA) functions as a catalyst.

Reporting their work were graduate student Travis Stams and Professor David Christianson of the University of Pennsylvania chemistry department; and Duke Medical Center postdoctoral fellow S. Niranjanakumari and Carol Fierke, associate professor of biochemistry. Their work is supported by the National Institutes of Health.

Ribonuclease P plays a key role in activating a molecule called transfer-RNA (tRNA) after it is first synthesized. Such tRNA molecules are the cellular equivalent of errand boys, latching onto individual subunits of proteins, called amino acids, to carry them to the cell's protein-making machinery, where the amino acids are chemically attached to one another in long stringlike molecules that fold into the cell's working proteins.

Specifically, ribonuclease P is a molecular scissors that helps turn a newly synthesized precursor into a functioning tRNA molecule by snipping off an extraneous segment at one end of the "pre-tRNA" molecule. Similarly, ribonuclease P helps activate another RNA, called ribosomal RNA, that is central to the cell's protein-making machinery.

In their experiments, the University of Pennsylvania researchers produced crystals of the ribonuclease P protein, and obtained the protein's structure through the widely used analytical method of X-ray crystallography. In this technique, an X-ray beam is directed through the protein crystal and is diffracted by the crystal's atoms into a pattern of spots. By analyzing the pattern, chemists can deduce the structure of the protein molecules that make up the crystal.

In analyzing the protein's structure, the biochemists found three regions where the protein could bind RNA. One region had an unusual topology and chemical characteristics that suggested it could be the place where the protein bound the RNA portion of the ribonuclease P enzyme.

However, another RNA-binding region of the protein consisted of a large cleft whose characteristics suggested it grabbed and held the segment of the pre-tRNA that was to be snipped off to produce the functioning tRNA.

These findings were particularly surprising, said the chemists, because most theories held that such proteins played only a structural role, helping fold the RNA into its active form, and not an active role in the catalytic chemical reaction.

"Before we had the structure, we had demonstrated that the protein was very important for binding of the pre-tRNA substrate," Fierke said, "but it wasn't important for binding tRNA. This binding could have been either an indirect effect, like changing the conformation of the RNA, or a direct effect. And in general it's been believed such proteins were only involved in folding the RNA, and not really involved in catalysis.

"But these data suggest that the end of the pre-tRNA snakes through that cleft, with the protein directly contacting the pre-tRNA. This is really a very different mechanism for what these proteins do," said Fierke.

The Duke researchers performed chemical experiments that confirmed this contact, producing altered versions of the protein that would chemically cross-link with the RNA in the cleft, allowing them to unequivocally determine that the protein was holding the RNA.

The Duke researchers also are tinkering with the protein's structure to explore a potential third key RNA binding region on the protein that may help the RNA of the ribonuclease P grab magnesium atoms that it needs to function optimally.

Such findings may offer intriguing insights into how the machinery of living cells first evolved, Fierke said.

"We really didn't expect such a role for the protein," she said. "And, if it turns out to be true, one could speculate that one of the reasons life evolved from an RNA-dependent world to a protein-dependent world is that the RNA required magnesium to do anything. And RNA is not particularly good at forming specific metal binding sites, whereas proteins are particularly good."

The biochemists' work might offer new targets for antibiotics, since ribonuclease P is essential for making all tRNAs, and since the bacterial enzyme is different from the enzyme in higher organisms. Thus, both the Duke and University of Pennsylvania groups propose to design inhibitor compounds that will block some aspect of the critical contacts among the protein, the RNA portion of the ribozyme, and the pre-tRNA.

"There are a great many places one could target to thwart this enzyme," Fierke said.

Story Source:

The above story is based on materials provided by Duke University. Note: Materials may be edited for content and length.

More From ScienceDaily

More Health & Medicine News

Featured Research

Mar. 3, 2015 — Scientists have discovered a new hormone that fights the weight gain caused by a high-fat Western diet and normalizes the metabolism -- effects commonly associated with exercising. When tested in ... full story

Mar. 3, 2015 — New assays can detect malaria parasites in human blood at very low levels and might be helpful in the campaign to eradicate malaria, reports a new study. An international team led by Ingrid Felger, ... full story

Mar. 3, 2015 — Adults over the age of 30 only catch flu about twice a decade, a new study suggests. So, while it may feel like more, flu-like illness can be caused by many pathogens, making it difficult to assess ... full story

Mar. 3, 2015 — No significant change in home habits of smokers have been observed in the aftermath of a ban on smoking in public spaces, researchers report. Greater inspiration to kick the habit likely comes from ... full story

Mar. 3, 2015 — Heart function has been associated with the development of dementia and Alzheimer's disease through a new study. Participants with decreased heart function, measured by cardiac index, were two to ... full story

Mar. 3, 2015 — Children of recently separated or divorced families are likelier to drink sugar-sweetened beverages than children in families where the parents are married, putting them at higher risk for obesity ... full story

Mar. 3, 2015 — Gastric bypass and similar stomach-shrinking surgeries are a popular option for obese patients looking to lose weight or treat type 2 diabetes. While the surgeries have been linked to a decreased ... full story

Mar. 3, 2015 — Most people consume more salt than they need and therefore have a higher risk of heart disease and stroke, which are the two leading causes of death worldwide. But a new study reveals that dietary ... full story

Featured Videos

Mom Triumphs Over Tragedy, Helps Other Families

AP (Mar. 3, 2015) — After her son, Dax, died from a rare form of leukemia, Julie Locke decided to give back to the doctors at St. Jude Children&apos;s Research Hospital who tried to save his life. She raised $1.6M to help other patients and their families. (March 3)
Video provided by AP

Looted and Leaking, South Sudan's Oil Wells Pose Health Risk

AFP (Mar. 3, 2015) — Thick black puddles and a looted, leaking ruin are all that remain of the Thar Jath oil treatment facility, once a crucial part of South Sudan&apos;s mainstay industry. Duration: 01:13
Video provided by AFP

Woman Convicted of Poisoning Son

AP (Mar. 3, 2015) — A woman who blogged for years about her son&apos;s constant health woes was convicted Monday of poisoning him to death by force-feeding heavy concentrations of sodium through his stomach tube. (March 3)
Video provided by AP

Related Stories

June 9, 2014 — Researchers explain how RNA molecules found in certain viruses mimic the shape of other molecules as part of a strategy to 'hijack' the cell and make more viruses. Viruses are worldwide ... full story

Oct. 28, 2013 — The protein LIMP-2 is vital for both humans and animals. If it is absent – due, for example, to a hereditary disease – substances of an unknown nature, probably lipids, accumulate in the ... full story

Oct. 9, 2012 — Experts in revealing molecular structure by X-ray crystallography have identified two new small "chaperone" molecules that may be useful in treating the inherited metabolic disorder known ... full story

Nov. 14, 2010 — In today's world of sophisticated organisms proteins are the stars. But long, long ago ribonucleic acid (RNA) reigned supreme. Now researchers have produced an atomic picture that shows how two ... full story

ScienceDaily features breaking news and videos about the latest discoveries in health, technology, the environment, and more -- from major news services and leading universities, scientific journals, and research organizations.